Raphael's Family
by TigerWolf12
Summary: Nine months, that was how long Raphael had been missing. Everyone had given him up for being dead, but not Leonardo, he knew his brother was still alive out there. This is a story about brothers, and the trials they face as a family. There will be canon pairings, but there will be NO incest of any kind.
1. Chapter 1

**Note:** This is a rewrite and continuation of a story that I had abandoned writing a couple years ago on the MNT Gaiden site. I was looking at my old sketchbooks, and the plot bunny for this story came back and bit me. I don't own the franchise.

I've always loved the Teenage Ninja Turtles; the first time I was introduced to them was through the live action movies in the 90's. Later I watched the 2003 series that 4kids created that followed a bit more closely to the Mirage comics. I have read the Mirage comics as well, and I have recently started to read the alternate take of the Turtles in the IDW comics. I have also watched the 2007 movie, and saw the Turtles forever movie. I have even started watching the 2012 series. My favorite turtle is Raphael, but I love his brothers as well, it's just that Raph has always stood out to me. This story is a mixture of my own, as well as the material that I followed over the years, please enjoy.

**Raphael's Family**

_Nine Months_

Leonardo looked at the Calendar; it had been nine months since Raphael went missing. He could not believe it had been so long, it was strange without his brother. Leonardo sat in his room, he did not want to join the rest of his family, and Master Splinter was out there with his brothers along with Casey and April. Master Splinter had built a shrine for Raphael, a picture that April had taken of his younger brother sat in the middle of the shrine. The picture was decorated with black ribbon, and his Sais rested next to them. Incense sat in the front of the picture, and the family had gathered to pay their final respects to the brother that was no longer there, all except Leonardo. Leonardo did not believe his brother was dead, so he did not want to join those that had given up on Raphael.

"I will find you, no matter what Raph." Leonardo vowed.

His thoughts drifted to his brother, and all that he knew about his disappearance. Raphael had gone through a growth spurt and grew to the height of six foot and had filled out to his fit his new large frame. During that time Raphael and he had gotten along a bit better, and insults were not thrown at each other as much. Master Splinter seemed happy that the two of them were getting along so well. The last time he saw his golden eyed brother was the day before all of their birthdays, Raphael had gone to meet Casey, but would not tell them why. Leonardo thought nothing of it, until an irate Casey called on the phone, he was angry that Raphael had blown him off, or so he thought. Leonardo remembered Donatello, who answered the phone; tell Casey that Raphael had left hours ago to meet up with him. That had raised a red flag, and before he could think, Leonardo had gone topside in search of his brother. He did not realize Donatello and Michelangelo had joined him. Casey had met them half way wearing his hockey mask and carrying his hockey stick.

The first day they had found something, in an alleyway they had seen a flash of light, and upon further investigation, had found Raphael's Sais. As they explored the area, Donatello had found a tranquilizer that was covered in blood. They had found nothing else, and had returned home. Donatello had run tests on the blood found, and confirmed what they all knew, that the blood belonged to Raph. The good news was that the blood that their brother had lost was not enough to kill him. Feeling hopeful, the brothers staked out the alleyway with Casey the next night, but came up with nothing else. They had spread out their search, and even visited their old enemies' hideouts to see if Raphael had been taken by one of them. They found nothing; it had seemed that Raphael had vanished from the face of the planet.

_Is the blood connected to his disappearance? _

During their search for Raphael, news reports all over the states had reported that blood from blood banks was being stolen. Even though they were not sure if Raph's disappearance with the blood banks being robbed were connected, they kept the possibility opened. Leonardo would spend the longest looking for his brothers, sometimes he was stay awake for forty eight hours in search of his brother. He only stopped for the brief time Donnie or Mikey took up the search where he left off. During his brother's disappearance, he had grown to five foot nine, and filled out to fit his new height. Donnie had grown to six foot one, but was thin and lanky. Mikey had grown to five foot seven, and had filled out like Raph and Leonardo had to his new height.

_Raph missed all that._

Days turned into weeks, and weeks turned into months. There still had been no leads to Raphael's whereabouts. That revelation had taken its toll on the family. Master Splinter would wait up all night until they returned from searching for Raph. Every time Raph was not with them, Master Splinter seemed to grow sadder. Leonardo saw Master Splinter enter his brother's room, and their father would sit on Raphael's bedroom floor looking at the things Raphael left behind. Leonardo himself had entered Raph's room, but did not touch anything; he did not want to disturb his brother's room. Donnie always stood in the door way leading to Raph's room, but would never enter. Mikey avoided the room all together, and would take the longer way around the lair so that he could avoid looking inside his brother's room.

_I am not ready to say goodbye, I know you are alive out there somewhere!_

When the eight month mark had hit on the date of Raph's disappearance, Master Splinter had taken them all aside, along with Casey and April. Leonardo remembered that day, his Sensei's eyes were too bright, and there was matted fur directly under his eyes. Master Splinter had told them that it was time to say their final respects to Raphael. Mikey had screamed and cried at Master Splinter, the youngest turtle did not want to say good bye. Donnie lowered his head, and seemed to accept the fact that his brother was gone, he had cried but did not let the others see. April began sobbing into Casey's chest, and the tears flowed from Casey's eyes. Leonardo refused to show any emotion, he could not believe that they had given up on their brother.

_After that they built that stupid shrine. Raphael is not dead!_

April and Casey helped Splinter build the shrine, while Splinter himself went through pictures of Raph to fine the right one for the shrine. Mikey stayed in his room during that time, and refused to come out to see the shrine being built for Raphael. Donnie had Raphael's Sais and was getting them prepared for display on the shrine. They built the shrine with great care, and it had taken a month to finish. Leonardo spent that time searching high and low for any sign of his brother. He had found nothing, but refused to give up.

_Why are they holding a funeral for someone who is not dead?_

They were out there right now saying their final goodbyes to Raph, Leonardo reflected, but he still refused to join them. April and Casey had worn black for Raph, and Donnie and Mikey had switched out their normal bandanas for black ones. Master Splinter had worn all white to Raph's 'funeral.' Leonardo listened as they each took turns saying goodbye to Raphael. After all was said and done, Donnie had entered Leonardo's room.

"I don't care how you feel, but isn't it a bit cruel not to attend your own brother's funeral?" Donnie snarled. "Mikey is crying in his room, because he thinks you hated Raph so much that you refused to acknowledge him at all!"

Leonardo sat up.

"He is not dead! I am not going to attend a so called funeral for a brother that is still alive!"

Donnie sagged against the doorframe.

"What would it take for you to acknowledge that Raph is no longer here?"

Leonardo looked into his brother's dark brown eyes.

"One more search."

"Leo, you can't…" Donnie began.

"One more search." Leonardo cut him off.

"Fine, let me get Mikey and Casey." Donnie replied.

Leonardo left his room, and saw Master Splinter comforting a crying April. He saw Donnie, Mikey, and Casey from the corner of his eye. Mikey's eyes were bloodshot from crying, and Casey was trying to make him laugh, but to no avail. Donnie looked tired, but he seemed to be refusing to cry for Mikey's sake. They all joined Leonardo, and followed him out of the lair, Leo saw Master Splinter watch them leave.

"We will have a stakeout in front of one of the blood banks." Leonardo told his group as they made their way along the rooftops.

"Leo, we never confirmed if the robbing of blood banks and Raph's disappearance were connected." Donnie told his brother.

"There was never any evidence that did not say it wasn't a possibility they were connected." Leonardo reminded him.

Donnie sighed, but did not say anything else.

The group reached their destination, and began to stake out the place. Mikey sat to the side, and Leonardo figured his youngest brother did not want to get his hopes up in finding Raph; he had been let down before. Donnie seemed to be not as enthused either; Leonardo remembered he had given up hope as finding Raph alive after the seventh month of Raph's disappearance. Casey was losing hope as well, over the months he had been just as obsessed at finding Raph, but now the reality of Raph's supposed death was starting to hit him. Leonardo was still obsessed at finding Raph, whether it was his corpse or not. He was not dead, Leonardo reminded himself.

"I managed to get some blood from under those idiots' noses. I pretended to be a doctor, and got what we needed, we can continue the experiments."

Leonardo's attention focused on the word 'experiment' and saw that his brothers and Casey had picked on that as well. Leonardo was one not to gloat, but there was a possibility he was right about the blood bank being linked to Raph's disappearance. As the truck the man entered started to speed away, they followed it from above. They followed the truck for over two hours, but it was worth it to Leonardo, if it led to Raphael. The men entered in what appeared to be an abandoned warehouse, they disappeared for a bit inside, then they came back out.

"We have a few other blood banks to hit tonight."

With that said, the two men got in their truck, and drove away from the warehouse. Once they were out of sight, Leonardo and the others stepped out of the shadows, and snuck inside the warehouse. The first thing that hit Leonardo was the sterile smell of medical supplies. He did not know exactly what they were, but they smelled a bit like the stuff that Donnie messed with when he patched up their injuries. The entire place was clean, but it was hard to tell with the low light they got from the lights above their heads.

"Oh my God!" Donnie suddenly exclaimed.

Leonardo turned around to scold him for shouting, but he realized that Donnie looked like whatever he saw made him sick. Leonardo turned in the direction his brother was looking in, and felt his stomach drop. There on a floor were corpses of baby mutated turtles. As Leonardo went over to the pile of corpses, he heard Casey swear as both Donnie and Mikey seemed to lose their composure. Leonardo investigated the corpses; some of the babies had hair, while others did not. Every baby was a different shade of green, and the number of fingers they had was different as well. Some had three fingers like them, while others had the same number of digits as a human did, some even seemed to be in between. Some of the baby mutants had no markings on their bodies, but Leonardo noticed that others, especially the bald ones, had a single pinprick in their arms.

"They must have been euthanized." Donnie said.

Donnie's voice revealed that same terror that Leonardo felt, but a small bit of hope stirred in his chest, Raph may be around.

Donnie, Casey, find something to put those babies in, we will give them a proper burial later. Mikey keep a look out, and stay out of here." Leonardo commanded.

Mikey did not need to be told twice, Leonardo winced as he heard his brother being sick just outside the door. Donnie and Casey immediately did what was asked of them, and Leonardo when deeper into the warehouse. Leonardo checked all the rooms, on the first floor, then the second floor. He found nothing, but he refused to give up. He went down to the basement, and saw a dungeon built into a wall. He saw the light reflecting off of something on the floor, and went over to it. To his surprise he saw a young baby mutated turtle, and he turned his head and saw more. All three babies had hair, and all three of them were feebly crawling all over the dungeon floor. Leonardo knelt down to touch one of the babies but something grabbed the baby, and blocked it from view.

"Don't touch her!" A raspy voice snarled from the shadows.

Although the voice was weak, Leonardo recognized it.

"Raphael!" Leonardo exclaimed.

"Leo?" The shadow shifted. "You finally found me, I knew you guys would."

Raphael pulled himself into the light, and Leonardo saw that he was in bad shape. Raphael's cheeks had sunk in, and he Leonardo could count all Raphael's ribs. Raphael's eyes appeared infected, and since Raphael crawled over to Leonardo with only the use of his arms, his legs must have been broken. Leonardo pulled out the T-phone, but before he could call anyone, the phone began to ring.

"Leo, one of the babies is still alive, he was buried underneath the other bodies, but he is still alive." Donnie told him.

"I found three more babies, and I found Raphael, he is alive." Leonardo told him.

There was a pause, and he heard two people crying in relief.

"Tell Casey I need his help, are you almost done with the rest of the babies?" Leonardo asked.

"Yes, Mikey found a huge truck, we are putting them in there, and Mikey is going to meet us at the entrance."

Leonardo said his goodbyes to his brother, and focused on Raphael and the three babies. The babies were weak, but they had survived this long, thanks to Raph. Leonardo used him Katanas to cut through the lock, and pulled Raph out first, then gathered the baby mutants. Casey arrived and Leonardo instructed him to carry the babies, he swung Raph over his shoulder in a fire man carry and they left the warehouse.

"All the babies are wrapped up, and in the back of the truck, we will give them a proper burial when we get back to town." Donnie told him.

Leonardo saw a baby mutant turtle in his arms.

"This was the only survivor out of the babies." Donnie told him.

"I found baby turtles with Raph." Leonardo told him.

Mikey slid over to the passenger side of the truck and held out his hands.

"Give the babies to me; I will keep them warm while you help Raph." Mikey told them.

Donnie and Leonardo handed the babies over to Mikey, and after that was done, Donnie climbed into the back. Leonardo gently passed Raphael to Donnie, and climbed in after them. Casey climbed into the driver's seat, and began the two hour ride back home.

_I knew you were alive._

**To be Continued…**


	2. Chapter 2

**Note:** Here is the next chapter to Raphael's Family, thank you for reading the first chapter. ^_^

**The Family increases by four**

Donatello took care of Raphael's injuries on the way back to the lair, Leonardo kept an eye on the bundled bodies of the unfortunate babies that did not make it, and Mikey was taking care of the babies. Casey was keeping an eye on the road as he drove back to the lair. Donatello concentrated on healing his older brother, his mind reeling with all the things that could have happened, and the grief that he had lost so many nieces and nephews. Although he would have to prove the babies' lineage, living and dead, to his brother the obvious evidence declared Raphael as their father.

_I wonder how Master Splinter will take it._

Donnie stared at his brother, relived that he was alive, he had given his brother up for dead, and he was glad that Leonardo had not given up on Raphael. As Donnie cleaned the wounds, he thought about the notebooks he had stolen from the lab that lay in the satchel at his side. He had found them before he had found the living baby under the pile of corpses. He still had not looked at them, since his brother and the babies were more important, but he planned to read them in detail when he got home to see if what happened to his brother and the babies would be revealed.

_They took his eye!_

Donnie's eyes widened when he had been treating his brother's eyes. His right eye had been infected, but a good ointment would bring it back to perfect condition. It was his left eye that made his stomach drop; his brother's left eye was gone. Donnie bandaged the eye, but did not mention it to Leonardo or Mikey yet, since he felt that it would be too distracting at the moment. Donnie concentrated on bandaging up his brother, and after he was done, he checked on Mikey to see if he did a good job on the living babies. Mikey had done a good job on taking care of the babies wounds, the wounds were not as severe as Raphael's, but all of the babies had bad eye infections. Except for little scraps, and tattoos on the inside of their right wrists, the eye infections were their worst injuries. Donnie checked the babies' weight, and realized that all of them were a healthy weight, except for the one he had found with the deceased babies. The one he found was a bit underweight.

_Raphael sacrificed his own health to keep the babies well fed._

Donnie patted each baby on the head when he was done checking on them. Two babies were female and two of them were males. One female baby had all five digits on each hand and foot, the same number of digits a normal human would have. One of the male babies had the same number of digits as the female. The male he had found had three fingers and a thumb, the same amount as the other female. He could not figure out why one baby was put with the deceased babies, while the female was left with Raphael, or left alive in general. It seemed that whoever done this to Raphael and the babies had a specific look in mind for all of them.

_No one has the right to decide who should live and who should die!_

Donnie gave one last look as the babies, he shook his head they were not just babies they were his nieces and nephews, before joining his brother Leonardo.

"Thank you for never giving up on Raph." Donnie told his brother.

Leonardo did not answer him right away.

"All these babies were Raphael's children weren't they." Leonardo finally said. "They are our nieces and nephews, but we will never get to know all of them, just four of them. Do you think Raphael met all his children?"

Donnie looked at Raphael, and then at the deceased babies, finally he turned to Leonardo.

"I hope not, because then Raphael would blame himself for their deaths, and never let go of that regret."

Donnie and Leonardo fell silent after that, Donnie eventually got up to check on Raphael, but no one spoke again for an hour.

"Guys, we're home."

Mikey's voice broke through Donnie's thoughts. Donnie realized that they were near the old abandoned warehouse that served as a decoy that protected the entrance to their home. Donnie pulled out the remote, and hit a button that revealed a false wall. Casey drove the truck into the warehouse, and Donnie closed the false wall. Mikey set to work opening up the manhole that lead to the sewers, while Leonardo and Donnie got Raph and the living babies ready to be transported to the sewers. Casey, Donnie, and Leonardo would return to fetch the deceased babies to properly prepare them for their burial.

"You know, I can ask my mom to lend some of her land for Raph's deceased babies, so they have a place to be buried." Casey told them.

Donnie saw Leonardo flinch.

"Thank you Casey that would mean a lot to us and Raphael." Donnie spoke for all his brothers.

"How do you think April and dad would respond to all of this?" Mikey asked.

No one had an answer for him.

Donnie and Leonardo lowered Raphael into the sewers and carried him to their lair. Mikey followed them carrying two babies, and Casey brought up the rear with the remaining babies. The process was silent, except for occasional instructions shared between Donnie and Leonardo on which would be the best path to take Raphael on that would not aggravate his injuries. Donnie and Leonardo reached the lair first.

"You found him!" April exclaimed.

Donnie and Leonardo nodded their heads to let her know they heard her, but they were focused on bringing Raphael safely into the lair. Master Splinter spotted them, and waved them over to his room. Donnie and Leonardo took that as an indication that Master Splinter wanted Raphael in his room. Once Raphael was settled down on to Master Splinter's bedroom floor, a voice interrupted all of their thoughts.

"They are so cute!" They heard April say.

Master Splinter looked had Donnie and Leonardo in confusion, then left the room.

"What is it?" Master Splinter asked, as he entered the main part of the lair.

Mikey and Casey brought the babies to Master Splinter, who began to study the babies in detail.

"Uh dad," Mikey began. "Those are not all the babies."

Master Splinter's eyes lit up, and April looked excited to meet more of the babies herself.

"Where are they?" Master Splinter asked.

"They are dead Sensei." Donnie answered.

Master Splinter's ears lowered in grief as he closed his eyes, and April put a hand over her mouth in shock as tears began to flow.

"Take me to them; I want to stay with them for a while." Master Splinter told them.

Leonardo guided Master Splinter up to the warehouse, where the truck resided with the deceased babies. Casey and April tended to the living babies, while Donnie went into his lab. Donnie wanted to go over the notes, and run some DNA tests to confirm what everyone knew, that the babies belonged to Raphael. Donnie had taken some DNA samples from the deceased babies, as well as the living babies. Now he ran the entire DNA through his machine, and began his research.

_Time to figure out what Raphael has been through, and how the babies are connected to him. _

After running his search for an hour, all of the babies' DNA confirmed that Raphael was the father to all of the babies. However, each maternal lineage to the babies was completely different. As Donnie looked at the mothers, he found out that each woman had visited the hospitals for blood work, or donated their blood for other reasons. Their blood each came from the places that had been robbed. Donnie confirmed the robbing of blood banks to Raphael's disappearance. He did the background for each baby that had died first, before moving to the living babies.

_The living babies were the most recent experiment; by this point all the flaws of hybrids were almost eliminated. Plus, whoever did this was getting the look that they wanted!_

Donnie began to focus on the living babies, and saw that one female, who was revealed to have black hair, was the oldest. Whoever ran the experiments had taken pictures of the living babies, and posted what they looked like. The baby's mother was not shown, it was implied that she did not exist, but the baby girl got her black hair from someone. The baby girl had Raphael's golden eye color and his tone of dark green skin as well.

_Her mother must have been a scientist who did this to Raph!_

Donnie made a note next to the notes that he had written for his black haired niece in his notebook. He researched the mothers for his other niece and nephews. His blonde haired nephew was next in age, followed by his brown haired niece. His nephew had the palest green skin out of all of them and had light blue eyes. His mother was a model who had donated her blood in hopes of saving someone's life. Her friend, who was a model and did the same, was the mother of his brown haired niece. His brown haired niece was almost as dark in skin color as her black haired sister, but she had bright green eyes instead of the golden ones.

_Time to run the DNA test on the last baby._

The last of the living babies was a the dark red haired nephew, he was the last born in the line of his siblings. He had lighter green skin than his sisters, but it was darker than his brother. He also had dark green eyes, and some freckles decorated his face. As Donnie scrolled to where the mother was, his eyes widened in shock.

_His mother is April!_

**To be Continued…**

**Note:** Here is the next chapter to Raphael's family. I am working on this as well as other fanfics. Thank you for reading, and I will see you in the next chapter. ^_^


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